Brain data#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
Archive:  neuromod-anat-brain-qmri.zip
  inflating: data/brain/results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/._results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/report-neuromod-anat-brain.html  
  inflating: data/brain/._report-neuromod-anat-brain.html  
  inflating: data/brain/neuromod-anat-brain.nextflow.log  
  inflating: data/brain/history-neuromod-anat-brain  
  inflating: data/brain/._history-neuromod-anat-brain  
  inflating: data/brain/timeline-neuromod-anat-brain.html  
  inflating: data/brain/._timeline-neuromod-anat-brain.html  
--2022-06-14 00:05:29--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000529Z&X-Amz-Expires=300&X-Amz-Signature=38e0771be3fe06bb5f9987801b94c45c86e13df4246d2d5ecd716556fcf336b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 00:05:29--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000529Z&X-Amz-Expires=300&X-Amz-Signature=38e0771be3fe06bb5f9987801b94c45c86e13df4246d2d5ecd716556fcf336b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  5% 20.4M 0s
    50K .......... .......... .......... .......... .......... 10% 99.6M 0s
   100K .......... .......... .......... .......... .......... 16% 65.5M 0s
   150K .......... .......... .......... .......... .......... 21%  138M 0s
   200K .......... .......... .......... .......... .......... 27%  117M 0s
   250K .......... .......... .......... .......... .......... 32%  124M 0s
   300K .......... .......... .......... .......... .......... 38%  132M 0s
   350K .......... .......... .......... .......... .......... 43%  115M 0s
   400K .......... .......... .......... .......... .......... 49%  130M 0s
   450K .......... .......... .......... .......... .......... 54%  142M 0s
   500K .......... .......... .......... .......... .......... 59%  138M 0s
   550K .......... .......... .......... .......... .......... 65%  136M 0s
   600K .......... .......... .......... .......... .......... 70%  139M 0s
   650K .......... .......... .......... .......... .......... 76%  141M 0s
   700K .......... .......... .......... .......... .......... 81%  132M 0s
   750K .......... .......... .......... .......... .......... 87%  118M 0s
   800K .......... .......... .......... .......... .......... 92%  135M 0s
   850K .......... .......... .......... .......... .......... 98%  140M 0s
   900K .......... .......                                    100%  101M=0.009s

2022-06-14 00:05:29 (95.5 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [939721/939721]

Load data plot it#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')
     subject  session acquisition  metric       unit label      mean  \
0          1        1     MP2RAGE   T1map     second    GM   1.48850   
1          1        1     MP2RAGE   T1map     second    WM   0.94136   
2          1        2     MP2RAGE   T1map     second    GM   1.46510   
3          1        2     MP2RAGE   T1map     second    WM   0.94620   
4          1        3     MP2RAGE   T1map     second    GM   1.28500   
..       ...      ...         ...     ...        ...   ...       ...   
123        6        4         NaN  MTRmap    percent    WM  53.09780   
124        6        4         MTS   MTsat  arbitrary    GM   8.51250   
125        6        4         MTS   MTsat  arbitrary    WM   8.55280   
126        6        4         MTS   T1map     second    GM   1.53840   
127        6        4         MTS   T1map     second    WM   1.01220   

           std    median      iqr  ...        q3  \
0      0.15877   1.48480  0.18402  ...   1.58070   
1      0.17416   0.87470  0.11626  ...   0.95667   
2      0.17762   1.47210  0.18738  ...   1.56700   
3      0.18076   0.87387  0.12917  ...   0.96739   
4      0.41732   1.41230  0.59626  ...   1.62630   
..         ...       ...      ...  ...       ...   
123    6.36400  54.32840  4.36430  ...  56.20390   
124  199.60140   1.72020  0.88756  ...   2.24390   
125  235.75970   4.07040  1.01800  ...   4.46410   
126    2.03670   1.73570  1.29400  ...   2.10790   
127    0.41837   1.03040  0.41547  ...   1.25520   

                                                   map  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
..                                                 ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...   

                                                  mask        software  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
..                                                 ...             ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   

                    date                                        map_basedon  \
0    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
1    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
2    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
3    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
4    2021-07-24 21:42:37                        sub-01_ses-003_UNIT1.nii.gz   
..                   ...                                                ...   
123  2021-07-24 22:57:39  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
124  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
125  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
126  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
127  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   

          runtime                   OS  \
0    Octave 5.2.0  x86_64-pc-linux-gnu   
1    Octave 5.2.0  x86_64-pc-linux-gnu   
2    Octave 5.2.0  x86_64-pc-linux-gnu   
3    Octave 5.2.0  x86_64-pc-linux-gnu   
4    Octave 5.2.0  x86_64-pc-linux-gnu   
..            ...                  ...   
123  Octave 5.2.0  x86_64-pc-linux-gnu   
124  Octave 5.2.0  x86_64-pc-linux-gnu   
125  Octave 5.2.0  x86_64-pc-linux-gnu   
126  Octave 5.2.0  x86_64-pc-linux-gnu   
127  Octave 5.2.0  x86_64-pc-linux-gnu   

                                        map_reference   data_type  
0    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
1    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
2    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
3    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
4    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
..                                                ...         ...  
123                                               NaN  derivative  
124                 https://doi.org/10.1002/mrm.21732  derivative  
125                 https://doi.org/10.1002/mrm.21732  derivative  
126                 https://doi.org/10.1002/mrm.21732  derivative  
127                 https://doi.org/10.1002/mrm.21732  derivative  

[128 rows x 23 columns]

White matter qMRI#

fig_wm = Plot(dataset, plot_name = 'brain-2')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')
     subject  session acquisition  metric       unit label      mean  \
0          1        1     MP2RAGE   T1map     second    GM   1.48850   
1          1        1     MP2RAGE   T1map     second    WM   0.94136   
2          1        2     MP2RAGE   T1map     second    GM   1.46510   
3          1        2     MP2RAGE   T1map     second    WM   0.94620   
4          1        3     MP2RAGE   T1map     second    GM   1.28500   
..       ...      ...         ...     ...        ...   ...       ...   
123        6        4         NaN  MTRmap    percent    WM  53.09780   
124        6        4         MTS   MTsat  arbitrary    GM   8.51250   
125        6        4         MTS   MTsat  arbitrary    WM   8.55280   
126        6        4         MTS   T1map     second    GM   1.53840   
127        6        4         MTS   T1map     second    WM   1.01220   

           std    median      iqr  ...        q3  \
0      0.15877   1.48480  0.18402  ...   1.58070   
1      0.17416   0.87470  0.11626  ...   0.95667   
2      0.17762   1.47210  0.18738  ...   1.56700   
3      0.18076   0.87387  0.12917  ...   0.96739   
4      0.41732   1.41230  0.59626  ...   1.62630   
..         ...       ...      ...  ...       ...   
123    6.36400  54.32840  4.36430  ...  56.20390   
124  199.60140   1.72020  0.88756  ...   2.24390   
125  235.75970   4.07040  1.01800  ...   4.46410   
126    2.03670   1.73570  1.29400  ...   2.10790   
127    0.41837   1.03040  0.41547  ...   1.25520   

                                                   map  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
..                                                 ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...   

                                                  mask        software  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
..                                                 ...             ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   

                    date                                        map_basedon  \
0    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
1    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
2    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
3    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
4    2021-07-24 21:42:37                        sub-01_ses-003_UNIT1.nii.gz   
..                   ...                                                ...   
123  2021-07-24 22:57:39  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
124  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
125  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
126  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
127  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   

          runtime                   OS  \
0    Octave 5.2.0  x86_64-pc-linux-gnu   
1    Octave 5.2.0  x86_64-pc-linux-gnu   
2    Octave 5.2.0  x86_64-pc-linux-gnu   
3    Octave 5.2.0  x86_64-pc-linux-gnu   
4    Octave 5.2.0  x86_64-pc-linux-gnu   
..            ...                  ...   
123  Octave 5.2.0  x86_64-pc-linux-gnu   
124  Octave 5.2.0  x86_64-pc-linux-gnu   
125  Octave 5.2.0  x86_64-pc-linux-gnu   
126  Octave 5.2.0  x86_64-pc-linux-gnu   
127  Octave 5.2.0  x86_64-pc-linux-gnu   

                                        map_reference   data_type  
0    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
1    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
2    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
3    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
4    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
..                                                ...         ...  
123                                               NaN  derivative  
124                 https://doi.org/10.1002/mrm.21732  derivative  
125                 https://doi.org/10.1002/mrm.21732  derivative  
126                 https://doi.org/10.1002/mrm.21732  derivative  
127                 https://doi.org/10.1002/mrm.21732  derivative  

[128 rows x 23 columns]